Tutorials

Tutorials are divided into two sections:

  • The Cookbook contains step-by-step instructions for performing common tasks, with detailed explanations of each step
  • In-depth includes longer discussions of issues that arise in high-throughput sequencing and genomics, and includes code examples when appropriate.

We suggest downloading the Demo dataset and following along.

Cookbook

Tutorial Contents
Setting up a genome for analysis Set up a genome for downstream analysis, using plastid or other toolkits
A simple alignment and quantitation workflow Simplified workflow of how to align sequencing data
Arrays of counts at each transcript position Retrieve a vector of high-throughput sequencing counts at each position in a transcript
Manipulating feature sequences Fetch the sequences of regions of interest (e.g. transcripts) from a genome
Gene expression & translation efficiency Compute gene expression measurements and translation efficicency using RNA-seq & ribosome profiling, and prepare data for differential expression analysis
Excluding (masking) regions of the genome Exclude specific regions – for example, repetitive genome sequence that gives rise to multimapping reads – from analysis. Discussion of mask files.
Creating custom BED, BigBed, and GTF2 annotation files Make a BED, BigBed, GTF2, or GFF3 file containing custom features.
Metagene analysis Perform metagene analysis, using ribosome profiling data at the start codon as an example. Then, develop metagene analysis around a custom landmark for use with other data types
Ribosomal P-site offsets Determine a P-site offset from ribosome profiling data
Read phasing in ribosome profiling Estimate read phasing (triplet periodicity) of ribosome profiling data
Plotting tools Demos of plotting tools in plastid.plotting

In-depth

Tutorial Contents
Categories and formats of genomics data Introduction & discussion to the types of data used in genomics, and the advantages and disadvantages of their various file formats
Coordinate systems used in genomics Primer on the various coordinate systems used in genomics
Ambiguous read alignments Issues arising when and strategies for handling multimapping reads
Read mapping functions In-depth discussion of mapping rules, with code examples of how to write your own mapping rule for your own sequencing data type